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Earth-96, the home of the Brandon Routh Superman, is likely given that distinction because of the publishing date for Kingdom Come, the series that gives us that version of the costume. The backstory of how the Planet was taken out was also lifted from Kingdom Come, and the newspaper about the gas attack, seen behind Clark Kent in one scene featured an illustration by Alex Ross (artist of Kingdom Come) and an article credited to Mark Waid (its writer).
Kevin Conroy discussed with Entertainment Weekly how the "Crisis" role took him by surprise, stating how the experience of playing Batman for the first time in live-action "threw him" at first. "I never approached this character from that physicalized aspect. I always just inhabited him with my voice," Conroy said. "When you do that in a recording studio, it's a very intimate experience and you're sort of living in your own imagination. You do it with your eyes closed and you're in this other world, and you have Mark Hamill feeding you [need], and the other actors (because we always recorded together in the booths.)" "To actually be on the set, in the physical world, and to be walking as the character and inhabiting the character in three dimensions, it was a real transition for me," he added. "It did take a while to get used to, I have to admit. I was surprised because I know the character so well."
Executive producer Marc Guggenheim spoke of Kevin Conroy, "He is stupendous, He is Bruce Wayne. [It's] just a lot of fun to see this actor who we all mainly know from voice work being on camera. It was really exciting." Conroy's appearance in "Crisis" is the result of a dream. "One of the things that was always on my bucket list is that I wanted to see old Bruce Wayne," says Guggenheim. "We talked about a variety of different casting possibilities, but [Legends of Tomorrow showrunner] Keto Shimizu, who is a huge animated Batman fan, pointed out that Kevin is the right age. We reached out to Kevin and he couldn't have been more lovely and more game for it."
Sara tells Harbinger that she promised her crew no more crossovers, a breaking the fourth wall joke referring to how the Legends weren't part of the Elseworlds crossover.
Earth-99 is a reference to when Batman Beyond came out in 1999. Kevin Conroy played an older Bruce Wayne (actually much older than this one), who took a new young man under his wing to make sure that there would always be the new Batman of the future.
The Earth-99 Bruce Wayne has mementos/trophies of a bloody Joker card, The Riddler's cane, Mr. Freeze's jar that contained the ice sculpture of his wife Nora Fries, and possibly a plant under glass that may signify Poison Ivy and the glasses of that Earth's Clark Kent.